Scipion-em-xmipptomo

- New protocols:
- apply_segmentation: Applies a segmentation to a set of tomograms.
- segment_morphology: Segments a tomogram by means of thresholding, different kind of filters and morphological operations.
- Protocols updated
- deep_misalignment: updated model, minor improvements
- extract_subtomos: improve extract subtomos readability
- Protocols fixed
- dose_filter: Dose filter, removing extract stacks
- More xmippTomo
- New xmippBase repository to manage shared protocols with Xmipp
- protocols deprecated: score_transform, denoising_confidence
- Removed tilt particles object (not used)

- Protocols updated
- applyAlignmentTS
- extract_particlesstacks: Added angles from Tilt Series
- extract_subtomos: Keeping directions in extract subtomos
- project_subtomograms: Added angles from Tilt Series
- deep_misalignment_detection: Update deep misalignment detection with new version of subtomo extraction and fiducial size options
- subtraction_subtomo: Improved implementation with MPI and md convert
- cltomo:
- resolution_local_monotomo: Allowing odd-even associated to the full tomogram
- Protocols fixed
- extract_particlestacks: Dose fixes
- deep_misalignment_detection: Recover deleted methods
- dose_filter: Dose validation fixed
- score_coordinates:
- More xmippTomo
- Fixed calculateRotationAngleAndShiftsFromTM
- Test refactoring

- New protocols
- project_subtomograms (for obtaining sobtomogram projections)
- extract_particlestacks (extract from tilt series and SetOfTiltSeriesParticle)
- denoising_confidence
- extract_particlestacks
- deep_misalignment_detection (misalignment detection in tomographic reconstructions from high-contrast regions)
- peak_high_contrast (for detecting high contrast regions in tomographic reconstruction)
- Protocols updated
- project_top: Subtomo projector compatible with hdf stacks. Test fixed. Projections keep orientation, Ignore alignments in projection
- subtomo_map_back, score_coordinates: Mapback scales any reference to match the tomogram sampling
- subtomo_map_back: Mapback waits now when scheduled and not the reference is needed, works with 3d classes, works with "other tomograms"
- project_subtomograms: Parallelized protocol
- Update requirements.txt
- Fix tests: protocol_extract_subtomos, monotomo, crop, resize, xmipptomo

- Map back fix: works with "other tomograms"

- Map back fix: works with 3d classes

- Mapback waits now when scheduled and not the reference is needed (validation added)